CT-AFM (Conductive Tip AFM) is commonly used for electrical characterization of organic and inorganic surface systems. Understanding electron transfer at the molecular level may lead to the development of molecular assemblies with unique properties and is of great importance for the advancement of both organic, molecular and bio-electronics. In this work we follow an approach to the study of Metal-molecule-Metal surface junctions that uses a combination of different AFM-based techniques. We first use nanografting to build nanopatches of the molecules of interest into a hosting reference self assembled monolayer (SAM) typically made of alkane and aromatic thiols. After the tip is changed to a conductive one, CT-AFM is used to characterize electrically the whole system recording, at the same time, the system topography. Some of the advantages of this approach are the possibility to build and study a wide range of different monolayers side-by-side on the same sample and the in-situ control of the quality both of the hosting monolayer and that of the grafted patches. Results will be presented on saturated and unsaturated thiols self-assembled and nanografted on Au(111) surfaces. We will also show a clear correlation between the contrast in current images and the quality of molecular packing inside the nanopatches.